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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ), 'gf_id' => 'HOM05D001439', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001439' ), 'data_identifier' => 'HOM05D001439', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001439', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '437', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p47410' => 'bna', 'A07p11210' => 'bna', 'A08p02880' => 'bna', 'A08p25510' => 'bna', 'A09p37620' => 'bna', 'Aa31LG5G3060' => 'aar', 'Aa31LG6G10940' => 'aar', 'Aa31sc565G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.274' => 'aag', 'Actinidia03300' => 'ach', 'Actinidia06779' => 'ach', 'Actinidia07602' => 'ach', 'Actinidia07830' => 'ach', 'Actinidia10999' => 'ach', 'Actinidia11000' => 'ach', 'Actinidia11111' => 'ach', 'Actinidia11112' => 'ach', 'Actinidia26141' => 'ach', 'Actinidia39477' => 'ach', 'Actinidia39478' => 'ach', 'Ah.04g162790' => 'amhyb', 'AL1G42050' => 'aly', 'AL8G15840' => 'aly', 'AL9U11900' => 'aly', 'Aqoxy1G03116' => 'aox', 'Aqoxy4G00628' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0SQJ2Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1H2VR5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31J8XM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.49JRJ0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH5A50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DG2K05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G6BTL7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P48F6M' => 'arhy', 'AT1G28420' => 'ath', 'AT4G12750' => 'ath', 'AT5G44180' => 'ath', 'ATR0730G134' => 'atr', 'ATR1098G049' => 'atr', 'Atru.chr10.1798' => 'acertr', 'Atru.chr6.2869' => 'acertr', 'Atru.chr6.3472' => 'acertr', 'AUR62035538' => 'cqu', 'AUR62036057' => 'cqu', 'AUR62037546' => 'cqu', 'AUR62038987' => 'cqu', 'BcaB03g12103' => 'bca', 'BcaB04g17209' => 'bca', 'BcaB07g33517' => 'bca', 'BcaC01g00060' => 'bca', 'BcaC01g01268' => 'bca', 'BcaC02g08708' => 'bca', 'BcaC05g26861' => 'bca', 'BcaC06g31644' => 'bca', 'BcaC06g34584' => 'bca', 'BcaC06g35369' => 'bca', 'BcaNung02981' => 'bca', 'BolC3t19784H' => 'bol', 'BolC3t21320H' => 'bol', 'BolC5t31459H' => 'bol', 'BolC7t42194H' => 'bol', 'BolC7t43215H' => 'bol', 'BraA06t27612Z' => 'bra', 'BraA07t28913Z' => 'bra', 'BraA08t32320Z' => 'bra', 'BraA08t34505Z' => 'bra', 'BraA09t39272Z' => 'bra', 'C03p75250' => 'bna', 'C03p90000' => 'bna', 'C04p51450' => 'bna', 'C05p27430' => 'bna', 'C07p16880' => 'bna', 'C07p26860' => 'bna', 'CAN.G1256.6' => 'can', 'CAN.G209.1' => 'can', 'CAN.G529.57' => 'can', 'CANSAT35G2047' => 'cansat', 'CANSAT56G1506' => 'cansat', 'CANSAT56G2417' => 'cansat', 'CANSAT64G0141' => 'cansat', 'CARHR027930' => 'chi', 'CARHR179080' => 'chi', 'CARHR218110' => 'chi', 'Carub.0001s2690' => 'cru', 'Carub.0007s3007' => 'cru', 'Carub.0008s0434' => 'cru', 'Ca_00363_v3' => 'car', 'Ca_17413_v3' => 'car', 'Ca_18589_v3' => 'car', 'Ca_18919_v3' => 'car', 'CBR_g17700' => 'cbr', 'Cc02_g09100' => 'ccan', 'Cc02_g13850' => 'ccan', 'Cc05_g07750' => 'ccan', 'CDE01G0356' => 'cde', 'CDE02G2880' => 'cde', 'CDE02G3848' => 'cde', 'CDE10G0226' => 'cde', 'CDE10G0974' => 'cde', 'CDE10G1047' => 'cde', 'CDE10G1054' => 'cde', 'Cfa000527' => 'cfa', 'Cfa002303' => 'cfa', 'Cfa002900' => 'cfa', 'Cfa014661' => 'cfa', 'Ciclev10014022m.g' => 'ccl', 'Ciclev10014023m.g' => 'ccl', 'Ciclev10014094m.g' => 'ccl', 'Ciclev10015005m.g' => 'ccl', 'Ciclev10017580m.g' => 'ccl', 'Ciclev10018240m.g' => 'ccl', 'CiPaw.03G181600' => 'cil', 'CiPaw.04G180000' => 'cil', 'CiPaw.04G180100' => 'cil', 'CiPaw.07G090300' => 'cil', 'CiPaw.09G063400' => 'cil', 'ClCG00G004780' => 'cla', 'ClCG01G023260' => 'cla', 'ClCG09G010560' => 'cla', 'COL.COLO4_19723' => 'col', 'COL.COLO4_31415' => 'col', 'Cpa.g.sc27.2' => 'cpa', 'Cpa.g.sc27.3' => 'cpa', 'Cpa.g.sc8.11' => 'cpa', 'Cpa.g.sc83.96' => 'cpa', 'Cpa.g.sc83.97' => 'cpa', 'Cre03.g174500' => 'cre', 'CsaV3_5G020680' => 'csa', 'CsaV3_6G050410' => 'csa', 'CsaV3_7G023680' => 'csa', 'CSS0016347' => 'camsi', 'CSS0026010' => 'camsi', 'CSS0043150' => 'camsi', 'CSS0047003' => 'camsi', 'DCAR_004044' => 'dca', 'DCAR_007998' => 'dca', 'DCAR_021265' => 'dca', 'DCAR_028055' => 'dca', 'DCAR_028382' => 'dca', 'Dinv05740' => 'din', 'Dinv05741' => 'din', 'Dinv05742' => 'din', 'Dinv06859' => 'din', 'Dinv17354' => 'din', 'Dinv29934' => 'din', 'Dinv30126' => 'din', 'Duzib132G0536' => 'dzi', 'Duzib133G1111' => 'dzi', 'Duzib138G1511' => 'dzi', 'Duzib160G0499' => 'dzi', 'Duzib235G0176' => 'dzi', 'ECA238G3650' => 'eca', 'EL10Ac4g08849' => 'bvu', 'EL10Ac9g20819' => 'bvu', 'Eucgr.D00596' => 'egr', 'Eucgr.K01058' => 'egr', 'Eucgr.K01361' => 'egr', 'FAN02G0189' => 'fan', 'FAN02G3093' => 'fan', 'FAN05G2787' => 'fan', 'FAN05G3838' => 'fan', 'FAN09G0293' => 'fan', 'FAN09G0796' => 'fan', 'FAN11G1486' => 'fan', 'FAN12G1448' => 'fan', 'FAN12G4075' => 'fan', 'FAN14G5546' => 'fan', 'FAN14G5737' => 'fan', 'FAN14G5823' => 'fan', 'FAN16G2831' => 'fan', 'FAN21G0276' => 'fan', 'FAN25G1066' => 'fan', 'FvH4_3g08620' => 'fve', 'FvH4_4g09960' => 'fve', 'FvH4_6g26700' => 'fve', 'FvH4_6g36260' => 'fve', 'Glyma.05G221500' => 'gma', 'Glyma.06G288900' => 'gma', 'Glyma.07G201200' => 'gma', 'Glyma.08G028000' => 'gma', 'Glyma.13G175200' => 'gma', 'Glyma.13G235300' => 'gma', 'Gohir.A06G211600' => 'ghi', 'Gohir.A06G211700' => 'ghi', 'Gohir.A11G145900' => 'ghi', 'Gohir.A12G139300' => 'ghi', 'Gohir.D06G209500' => 'ghi', 'Gohir.D06G209600' => 'ghi', 'Gohir.D11G152000' => 'ghi', 'Gohir.D12G143800' => 'ghi', 'Gorai.007G162700' => 'gra', 'Gorai.008G155100' => 'gra', 'Gorai.010G243500' => 'gra', 'Gorai.010G256900' => 'gra', 'GSVIVG01020605001' => 'vvi', 'GSVIVG01021113001' => 'vvi', 'GSVIVG01036776001' => 'vvi', 'HanXRQChr03g0072381' => 'han', 'HanXRQChr04g0117141' => 'han', 'HanXRQChr07g0200581' => 'han', 'HanXRQChr14g0455641' => 'han', 'HanXRQChr15g0469531' => 'han', 'HanXRQChr15g0481491' => 'han', 'HanXRQChr17g0554611' => 'han', 'Haze_06382' => 'cav', 'Haze_13244' => 'cav', 'Haze_24510' => 'cav', 'Hma1.2p1_0345F.1_g131230' => 'hma', 'Hma1.2p1_0345F.1_g131250' => 'hma', 'Hma1.2p1_0558F.1_g178470' => 'hma', 'Hma1.2p1_1100F.1_g257130' => 'hma', 'HPP92_023234' => 'vpl', 'HPP92_023235' => 'vpl', 'HPP92_023277' => 'vpl', 'HPP92_023278' => 'vpl', 'HPP92_025328' => 'vpl', 'HPP92_025329' => 'vpl', 'Hund01014' => 'sun', 'Hund07869' => 'sun', 'Hund22225' => 'sun', 'Lalb_Chr05g0223731' => 'lal', 'Lalb_Chr09g0331921' => 'lal', 'Lalb_Chr15g0089681' => 'lal', 'Lalb_Chr16g0384011' => 'lal', 'Lalb_Chr18g0059381' => 'lal', 'Lalb_Chr20g0121581' => 'lal', 'Lj1C693T2' => 'lonja', 'Lj1C693T3' => 'lonja', 'Lj1C693T4' => 'lonja', 'Lj1C697G7' => 'lonja', 'Lj2A362T44' => 'lonja', 'Lj2C292T8' => 'lonja', 'Lj2C38G11' => 'lonja', 'Lj2C38T11' => 'lonja', 'Lj3g0019816' => 'lja', 'Lj4g0015660' => 'lja', 'Lj4g0024460' => 'lja', 'Lj6g0010323' => 'lja', 'Lsat_1_v5_gn_2_107580' => 'lsa', 'Lsat_1_v5_gn_6_65401' => 'lsa', 'Lsat_1_v5_gn_7_22781' => 'lsa', 'Lsat_1_v5_gn_8_133600' => 'lsa', 'Lsat_1_v5_gn_9_26120' => 'lsa', 'Manes.12G058700' => 'mes', 'Manes.13G141800' => 'mes', 'Manes.17G049300' => 'mes', 'Mapoly0005s0159' => 'mpo', 'MBI18_g11240_MAGBIO' => 'mbi', 'MCO02G503' => 'mco', 'MCO06G017' => 'mco', 'MD05G1310200' => 'mdo', 'MD09G1170800' => 'mdo', 'MD10G1289100' => 'mdo', 'MD17G1156400' => 'mdo', 'Medtr2g014490' => 'mtr', 'Medtr4g078860' => 'mtr', 'Medtr4g088375' => 'mtr', 'MELO3C007260.2' => 'cme', 'MELO3C024106.2' => 'cme', 'Migut.F00815' => 'egut', 'Migut.H01470' => 'egut', 'Migut.M01107' => 'egut', 'MSTRG.14322' => 'ama', 'MSTRG.7359' => 'ama', 'MSTRG.9006' => 'ama', 'MSTRG.9529' => 'ama', 'Nitab4.5_0000621g0070' => 'nta', 'Nitab4.5_0001955g0100' => 'nta', 'Nitab4.5_0003799g0010' => 'nta', 'Nitab4.5_0004359g0020' => 'nta', 'Nitab4.5_0005191g0050' => 'nta', 'Nitab4.5_0005417g0010' => 'nta', 'Nn1g04237' => 'nnu', 'Nn1g06413' => 'nnu', 'Nn4g24992' => 'nnu', 'Nn5g28132' => 'nnu', 'Nn5g28133' => 'nnu', 'Oeu012153.2' => 'oeu', 'Oeu012227.1' => 'oeu', 'Oeu016006.1' => 'oeu', 'Oeu016007.1' => 'oeu', 'Oeu016030.1' => 'oeu', 'Oeu056520.3' => 'oeu', 'Os01g0672201' => 'osa', 'Os01g0672300' => 'osa', 'Os05g0562400' => 'osa', 'Os07g0619600' => 'osa', 'Peaxi162Scf00120g00521' => 'pax', 'Peaxi162Scf00845g00120' => 'pax', 'Peaxi162Scf00926g00006' => 'pax', 'Peaxi162Scf01018g00118' => 'pax', 'PGR004G2384' => 'pgr', 'PGR044G2616' => 'pgr', 'PGR142G1802' => 'pgr', 'PGSC0003DMG400000999' => 'stu', 'PGSC0003DMG400009397' => 'stu', 'PGSC0003DMG400031766' => 'stu', 'Phvul.002G232200' => 'pvu', 'Phvul.002G303200' => 'pvu', 'Phvul.006G182000' => 'pvu', 'Potri.004G048675' => 'ptr', 'Potri.007G135500' => 'ptr', 'Potri.011G057700' => 'ptr', 'Potri.014G173300' => 'ptr', 'Potri.017G016200' => 'ptr', 'Pp3c15_13310' => 'ppa', 'Pp3c16_15110' => 'ppa', 'Pp3c16_15118' => 'ppa', 'Pp3c9_18520' => 'ppa', 'Prupe.3G029100' => 'ppe', 'Prupe.3G029400' => 'ppe', 'Prupe.4G052600' => 'ppe', 'Psat0s3732g0080' => 'psa', 'Psat1g202960' => 'psa', 'Psat1g203000' => 'psa', 'Psat2g060720' => 'psa', 'Psat6g093800' => 'psa', 'Psat7g021400' => 'psa', 'Psat7g116080' => 'psa', 'Psat7g167560' => 'psa', 'Psat7g201640' => 'psa', 'Psat7g201720' => 'psa', 'PSO063G6089' => 'pso', 'PSO210G6356' => 'pso', 'PSO782G0625' => 'pso', 'PSO832G3479' => 'pso', 'QL04p042996' => 'qlo', 'QL04p082212' => 'qlo', 'QL05p042276' => 'qlo', 'QL05p042429' => 'qlo', 'QL08p040227' => 'qlo', 'QL08p040265' => 'qlo', 'QL11p007061' => 'qlo', 'RcHm_v2.0_Chr2g0127081' => 'rch', 'RcHm_v2.0_Chr2g0127091' => 'rch', 'RcHm_v2.0_Chr2g0148261' => 'rch', 'RcHm_v2.0_Chr4g0406751' => 'rch', 'RcHm_v2.0_Chr5g0009221' => 'rch', 'Rhsim02G0134900' => 'rsi', 'Rhsim06G0136900' => 'rsi', 'Rhsim09G0138700' => 'rsi', 'RhsimUnG0013600' => 'rsi', 'Sabra04G0030600' => 'sbr', 'Sabra07G0109800' => 'sbr', 'Sabra11G0039900' => 'sbr', 'Sabra14G0132600' => 'sbr', 'Sabra17G0012700' => 'sbr', 'SalBow3G1926' => 'sbo', 'SalBow3G2022' => 'sbo', 'SalBow7G2291' => 'sbo', 'Sc09g0004660' => 'sci', 'Sc12g0003230' => 'sci', 'Sed0000156' => 'sed', 'Sed0010792' => 'sed', 'Sed0014026' => 'sed', 'SEGI_01020' => 'sgi', 'SEGI_12627' => 'sgi', 'SEGI_13942' => 'sgi', 'SEGI_16610' => 'sgi', 'SEGI_19944' => 'sgi', 'SEGI_20521' => 'sgi', 'SEGI_28384' => 'sgi', 'SEGI_30380' => 'sgi', 'SEGI_31911' => 'sgi', 'SEGI_39795' => 'sgi', 'SGA_v2.0_scaffold16G07637' => 'sas', 'SGA_v2.0_scaffold22G09664' => 'sas', 'SGA_v2.0_scaffold34G13921' => 'sas', 'SGA_v2.0_scaffold70G23491' => 'sas', 'SHI01532' => 'shi', 'SHI01533' => 'shi', 'SHI01534' => 'shi', 'SHI01535' => 'shi', 'SHI10198' => 'shi', 'SMO228G0061' => 'smo', 'SMO228G0122' => 'smo', 'SMO337G0095' => 'smo', 'Solyc02g077660.3' => 'sly', 'Solyc07g053610.3' => 'sly', 'Solyc11g006200.2' => 'sly', 'Sopen02g022560' => 'spe', 'Sopen07g027560' => 'spe', 'Sopen11g002130' => 'spe', 'Sp1g24700' => 'spa', 'Sp2g09000' => 'spa', 'Sp7g09140' => 'spa', 'TAR375G1143' => 'tar', 'TAR626G0101' => 'tar', 'TAR626G0121' => 'tar', 'TAR627G0298' => 'tar', 'THA.LOC104801160' => 'tha', 'THA.LOC104812616' => 'tha', 'THA.LOC104814231' => 'tha', 'THA.LOC104815378' => 'tha', 'THA.LOC104826040' => 'tha', 'THA.LOC104826638' => 'tha', 'Thecc.01G203900' => 'tca', 'Thecc.02G186300' => 'tca', 'Thecc.06G181000' => 'tca', 'Thhalv10003131m.g' => 'esa', 'Thhalv10003435m.g' => 'esa', 'Thhalv10006543m.g' => 'esa', 'Thhalv10024262m.g' => 'esa', 'TPR.G11655' => 'tpr', 'TPR.G19912' => 'tpr', 'TPR.G22823' => 'tpr', 'TPR.G9356' => 'tpr', 'TWI14G1311' => 'twi', 'TWI18G1300' => 'twi', 'TWI23G0951' => 'twi', 'TWI36G0060' => 'twi', 'TWI38G1102' => 'twi', 'TWI38G1950' => 'twi', 'unitig_27.g24975' => 'ugi', 'unitig_37.g12875' => 'ugi', 'unitig_37.g12876' => 'ugi', 'unitig_46.g18727' => 'ugi', 'vmacro10348' => 'vma', 'vmacro12346' => 'vma', 'vmacro15932' => 'vma', 'VMungo0251G2358' => 'vmu', 'VMungo0251G2748' => 'vmu', 'VMungo0251G2955' => 'vmu', 'VMungo0540G1437' => 'vmu', 'VMungo1127G0214' => 'vmu', 'Zm00001eb061430' => 'zma', 'Zm00001eb153390' => 'zma', 'Zm00001eb157190' => 'zma', 'Zm00001eb157200' => 'zma', 'Zm00001eb157210' => 'zma', 'Zm00001eb157220' => 'zma', 'Zm00001eb157230' => 'zma', 'Zm00001eb295800' => 'zma', 'Zm00001eb343660' => 'zma', 'Zm00001eb359990' => 'zma', 'Zm00001eb423620' => 'zma', 'Zm00001eb423630' => 'zma' ) $gf_id = 'HOM05D001439' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001439' ) $data_identifier = 'HOM05D001439' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 11, 'amhyb' => (int) 1, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 5, 'eca' => (int) 1, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 8, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mco' => (int) 2, 'mdo' => (int) 4, 'mtr' => (int) 3, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 10, 'pso' => (int) 4, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 10, 'sas' => (int) 4, 'shi' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 12 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb423630' $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